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emmanuelparadis / ape

analysis of phylogenetics and evolution
http://ape-package.ird.fr/
GNU General Public License v2.0
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Add write.phyloXML() and corresponding tests #120

Closed fmarotta closed 3 weeks ago

fmarotta commented 4 months ago

Hi! This PR adds a function to export trees in PhyloXML format (and some tests).

emmanuelparadis commented 3 months ago

Hi Federico,

This sounds interesting! Right now, a help page (*.Rd) is missing. Also we removed the tests/ folder from the ape's sources because the tests take too long to run for CRAN: see the package apeTests where tests are now run.

There are some information on how to prepare contribution to ape on:

https://emmanuelparadis.github.io/ape_development.html

This needs a bit of updating (I'll add the point about apeTests). If possible too, I'll try to add information about adding dependencies: so far ape tries to use simple dependencies (i.e., R + recommended packages).

Best,

Emmanuel

fmarotta commented 3 months ago

Hi Emmanuel, thanks a lot for your reply!

I have moved the tests to the apeTests repository and added a .Rd file for documentation. This PR only adds one suggested dependency, xml2. We could live without it and create the XML elements with paste(), but it would be a bit uglier. Also, an XML-parsing package would be definitely needed if someone wants to implement read.phyloXML() in the future. Still, I will remove the dependency if you prefer so.

I have incremented the version from 5.8-0.1 to 5.8-1.0. I didn't find any info about the convention for minor versions and patches, so please let me know if the number is not correct.

Federico

emmanuelparadis commented 3 weeks ago

Hi Federico,

Sorry for taking so long to get back to this.

Many thanks for the updated PR. I added the changes manually because other changes were made in the meantime.

This PR only adds one suggested dependency, xml2.

OK with that. We can see how it works.

I have incremented the version from 5.8-0.1 to 5.8-1.0. I didn't find any info about the convention for minor versions and patches, so please let me know if the number is not correct.

Actually, it is explained on another page. No worry, I changed it to "Version: 5.8-0.4". I also adapted a few other files (you can add your ORCID number if you wish in the DESCRIPTION file).

I'll push everything here in a moment. apeTests has also been updated.

Cheers,

Emmanuel

fmarotta commented 18 hours ago

Thank you Emmanuel!